Maresa Fagan: Testing times keeping up with demand

Microbiology laboratories are now running Covid-19 tests day and night writes Maresa Fagan
Maresa Fagan: Testing times keeping up with demand
Dr. James O’Connor, senior medical scientist and Liz Fitzpatrick, chief medical scientist working on Covid-19 sample preparation in the microbiology laboratory at the Mercy University Hospital, Cork. Picture: Dan Linehan

Microbiology laboratories are now running Covid-19 tests day and night writes Maresa Fagan

Medical scientists working in laboratories across the country are among the unseen heroes working in the background of the Covid-19 response.

The team at Mercy University Hospital in Cork was among the legions of laboratory staff who reacted quickly to the emerging biological threat to roll out Covid-19 testing for patients and frontline staff in local hospitals.

While the pandemic brought challenges it also brought out the best in people, according to chief medical scientist, Liz Fitzpatrick, and senior medical scientist, Dr James O’Connor, who were in the eye of the storm at the hospital’s microbiology department when the public health emergency struck.

The past two months have been something of a roller-coaster ride, the medical scientists say, and while there have been challenges there have been many rewards and highlights along the way too.

Since Covid-19 arrived the Mercy team, which works alongside consultant microbiologists Dr Deirdre O’Brien and Dr Aoife Ronayne, have been working night and day to get a new test for this new virus up and running and also to see off challenges, like reagent shortages, that were affecting labs all over the world.

Time too was in short supply, as Liz explains: “As scientists we tend to be quite conservative and take our time to get a new test up and running but with Covid-19 we didn’t have that luxury. Under normal circumstances it would probably have taken six months to get that test up and running but we have gotten through this much more quickly.”

Covid19- samples are added to the reagent for testing  in the microbiology laboratory at the Mercy University Hospital, Cork. Pictue Dan Linehan
Covid19- samples are added to the reagent for testing in the microbiology laboratory at the Mercy University Hospital, Cork. Pictue Dan Linehan

Luckily the Mercy Hospital had the necessary equipment at its disposal, a Seegene analyser, which enabled Liz and her team to firstly validate the Covid-19 test and then get testing up and running.

The equipment was procured through a Slaintecare Integration Fund, a Department of Health initiative, to carry out tests for bacteria, such as E. Coli and salmonella, and viruses and was now being repurposed for Covid-19 testing.

The hospital laboratory, James said, was fortunate to be able to “adapt the technology to good effect”.

Liz added: “We were very well placed to react to this crisis. It is state-of-the-art equipment that detects bacterial or viral DNA or RNA directly from samples and cuts down turnaround times hugely.”

The team spent about two weeks training staff to use the equipment, sourcing materials and addressing IT and clerical issues but was delayed by a global shortage of reagents needed to carry out the test.

At one point the demand for reagent saw James and other team members drive halfway across the country to get their hands on the sought after chemicals that were arriving via Dublin port.

The team was also grateful when CIT, UCC, and Pfizer stepped in to bridge the supply gap.

“It was extremely generous of Pfizer to send their supply of lysis buffer to us. It meant that we could hit the ground running and it gave us enough to test around 400 samples and complete the initial validation run,” James explained.

Once reagents became available, it took three to four long days at the bench to validate the first run of coronavirus samples.

Throughout the Covid-19 response, hospital laboratories across the country networked and co-operated to overcome supply issues and the HSE’s National Programme for Clinical Pathology was also a valuable source of support, Liz said, adding that reagent supplies were being continually monitored.

Dr. James O’Connor, senior medical scientist and Liz Fitzpatrick, chief medical scientist workinng on Covid-19 sample preparation and testing in the micro biology laboratory at the Mercy University Hospital, Cork. Picture: Dan Linehan
Dr. James O’Connor, senior medical scientist and Liz Fitzpatrick, chief medical scientist workinng on Covid-19 sample preparation and testing in the micro biology laboratory at the Mercy University Hospital, Cork. Picture: Dan Linehan

The Mercy Foundation also supported the lab by funding three new microbiological safety cabinets needed to ensure the health and safety of staff working with viral samples.

Since going live with Covid-19 testing on March 24 the lab is providing a round-the-clock dedicated service that can turn around results within 24 hours. The lab is also managing a routine workload testing for other viruses and bacteria.

“We have recruited extra staff. We now provide a dedicated microbiology service, running Covid tests day and night, seven days a week,” Liz said.

In addition to running Covid-19 tests for patients and staff at the Mercy Hospital the lab also runs tests for Kerry General Hospital, South Infirmary, and Mater Private hospitals.

Covid-19 tests will become the norm for the micro lab into the future as the test is now part of routine pre-assessment for patients undergoing surgery. “Covid-19 testing is here to stay. It’s going to be part of our routine workload going forward,” Liz said.

Staff at the hospital are also trialling antibody tests for Covid-19, which can detect if individuals had contracted the virus in the past.

Antibody tests are expected to be rolled out later this summer as part of a national study to determine how prevalent Covid-19 is in the general population.

The Health Protection Surveillance Centre is currently drafting a plan to roll out the antibody study once tests have been validated and selected.

The scientists say they were buoyed by the “extraordinary” goodwill and support shown by staff, the community, and businesses. “It has brought out the best in everybody,” Liz said.

She said staff across every department and section of the hospital contributed to the Covid-19 response: “It has felt like a massive team effort with everybody doing whatever they can and asking ‘what else can I do to make this work? It’s been amazing”.

The reagent used in the testing of Covid19- samples in the microbiology laboratory at the Mercy University Hospital, Cork. Picture: Dan Linehan
The reagent used in the testing of Covid19- samples in the microbiology laboratory at the Mercy University Hospital, Cork. Picture: Dan Linehan

Members of the public also showed their support by sending in postcards, which are proudly displayed on a notice board at the hospital, while local businesses lifted spirits with deliveries of cakes, sandwiches, and other food. “It gives you a bit of a gee-up to think that people are thinking of us and that you’re not in this on your own,” Liz said.

Liz and James also singled out Blood Bike for special mention for making sure that samples arrived safely at the National Virus Reference Laboratory in Dublin.

“In my 35 years working in medical laboratories I have never encountered anything like this in terms of the speed at which everything has happened and the pressure to get it up and running,” Liz said.

“It’s been challenging but it’s been extremely rewarding as well to be able to play a part in this international crisis and hopefully make some difference in the fight against coronavirus,” she added.

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